Triploids, recognized to occur more frequently in natural and experimental populations of many species than previously appreciated, display important economic and biological values. Despite this, however, linkage analysis for triploids has not been well explored. We develop a statistical model for estimating and testing the linkage between molecular markers in a triploid population derived from a tetraploid and diploid parent. The model incorporates one important meiotic feature of tetraploids by which more homologous chromosomes pair with a greater likelihood than less homologous chromosomes. By implementing the EM algorithm within the maximum likelihood framework, the model provides a procedure for simultaneous estimation of the linkage and preferential pairing factor. The model accommodates the segregating patterns of pseudotest markers and intercross markers with different amounts of informativeness. The utility of the model was validated through a real data analysis and simulation studies. The model provides a statistical tool for linkage analysis in a triploid population by taking into account meiotic behavior of tetraploids. Results from the model will help to shed light on the genetic diversity and origin of a polyploid population.
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